Levi A. Garraway
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View article: Smoking habit and long-term colorectal cancer incidence by exome-wide mutational and neoantigen loads: evidence based on the prospective cohort incident-tumour biobank method
Smoking habit and long-term colorectal cancer incidence by exome-wide mutational and neoantigen loads: evidence based on the prospective cohort incident-tumour biobank method Open
Objective To test the hypothesis that the association of smoking with long-term colorectal cancer incidence may be stronger for tumours with higher mutational and neoantigen loads. Methods and analysis In the Nurses’ Health Study (1980–201…
View article: Real-time genomic characterization of advanced pancreatic cancer to enable precision medicine
Real-time genomic characterization of advanced pancreatic cancer to enable precision medicine Open
Clinically relevant subtypes exist for pancreatic ductal adenocarcinoma (PDAC), but molecular characterization is not yet standard in clinical care. We implemented a biopsy protocol to perform time-sensitive whole-exome sequencing and RNA …
View article: Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbView
Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbView Open
Optical pooled screening (OPS) is a highly scalable method for linking image-based phenotypes with cellular perturbations. However, it has thus far been restricted to relatively low-plex phenotypic readouts in cancer cell lines in culture,…
View article: A compendium of Amplification-Related Gain Of Sensitivity (ARGOS) genes in human cancer
A compendium of Amplification-Related Gain Of Sensitivity (ARGOS) genes in human cancer Open
Chromosomal gains are among the most frequent somatic genetic alterations occurring in cancer. While the effect of sustained oncogene expression has been characterized, the impact of copy-number gains affecting collaterally-amplified “byst…
View article: Supp. Table S21 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer
Supp. Table S21 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer Open
Supplementary Table S21: Segmented copy-number ratios
View article: Supplementary Figure 1 from Activating mTOR Mutations in a Patient with an Extraordinary Response on a Phase I Trial of Everolimus and Pazopanib
Supplementary Figure 1 from Activating mTOR Mutations in a Patient with an Extraordinary Response on a Phase I Trial of Everolimus and Pazopanib Open
PDF file 249K, Effect of pazopanib on S6K1 phosphorylation in cells expressing activating MTOR mutations
View article: Supp. Table S2 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer
Supp. Table S2 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer Open
Supplementary Table S2: Somatic mutations
View article: Supp. Table S2 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer
Supp. Table S2 from Genetic Mechanisms of Immune Evasion in Colorectal Cancer Open
Supplementary Table S2: Somatic mutations
View article: Data from Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function <i>ERF</i> Mutations
Data from Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function <i>ERF</i> Mutations Open
African-American men have the highest incidence of and mortality from prostate cancer. Whether a biological basis exists for this disparity remains unclear. Exome sequencing (n = 102) and targeted validation (n = 90) of localized primary h…
View article: Supplemental Figure 8 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer
Supplemental Figure 8 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer Open
Figure S8
View article: Supplemental Figure 7 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer
Supplemental Figure 7 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer Open
Figure S7
View article: Supplementary Table S6 from Systematic Interrogation of 3q26 Identifies <i>TLOC1</i> and <i>SKIL</i> as Cancer Drivers
Supplementary Table S6 from Systematic Interrogation of 3q26 Identifies <i>TLOC1</i> and <i>SKIL</i> as Cancer Drivers Open
Supplementary Table S6 - XLSX file 8K, Primers used for generating TLOC1 truncation mutants
View article: Supplementary Data from MAPK Pathway Suppression Unmasks Latent DNA Repair Defects and Confers a Chemical Synthetic Vulnerability in <i>BRAF-, NRAS</i>-, and <i>NF1</i>-Mutant Melanomas
Supplementary Data from MAPK Pathway Suppression Unmasks Latent DNA Repair Defects and Confers a Chemical Synthetic Vulnerability in <i>BRAF-, NRAS</i>-, and <i>NF1</i>-Mutant Melanomas Open
Supplementary Tables 1-3
View article: Supplementary Figures from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers
Supplementary Figures from Frequent Mutation of the PI3K Pathway in Head and Neck Cancer Defines Predictive Biomarkers Open
Supplementary Figures - PDF file 441K, Four figures as follows: SF1: decreased PTEN expression in HNSCC with PTEN loss. SFs 2-4: PIK3CA mutant HNSCC tumorgrafts treatment response characterization; PI3K inhibitors +/- cetuximab, tumor meas…
View article: Data from MAP Kinase Pathway Alterations in <i>BRAF</i>-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition
Data from MAP Kinase Pathway Alterations in <i>BRAF</i>-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition Open
Treatment of BRAF-mutant melanoma with combined dabrafenib and trametinib, which target RAF and the downstream MAP–ERK kinase (MEK)1 and MEK2 kinases, respectively, improves progression-free survival and response rates compared with dabraf…
View article: Supplementary Table S1 from Clinical Acquired Resistance to RAF Inhibitor Combinations in <i>BRAF</i>-Mutant Colorectal Cancer through MAPK Pathway Alterations
Supplementary Table S1 from Clinical Acquired Resistance to RAF Inhibitor Combinations in <i>BRAF</i>-Mutant Colorectal Cancer through MAPK Pathway Alterations Open
Supplementary Table S1. Patient characteristics and MAPK pathway reactivating resistance mechanisms of BRAF-mutant CRC patients with clinical acquired resistance to RAF/EGFR or RAF/MEK inhibitor combinations.
View article: Supplementary Table 1 from Reactivation of ERK Signaling Causes Resistance to EGFR Kinase Inhibitors
Supplementary Table 1 from Reactivation of ERK Signaling Causes Resistance to EGFR Kinase Inhibitors Open
PDF file - 74K, Table describing clinical and molecular characteristics of NSCLC patients
View article: Supplemental Figures from Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function <i>ERF</i> Mutations
Supplemental Figures from Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function <i>ERF</i> Mutations Open
Supplemental Figure 1. Copy number alterations of AAPC exome set. Supplemental Figure 2. Copy number analysis grouped by Gleason scores. Supplemental Figure 3. Recurrent somatic copy number alterations in the AAPC cohort. Supplemental Figu…
View article: Supplemental Table 2 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer
Supplemental Table 2 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer Open
Supplemental Table 2
View article: Supplementary Figure 1 from Activating mTOR Mutations in a Patient with an Extraordinary Response on a Phase I Trial of Everolimus and Pazopanib
Supplementary Figure 1 from Activating mTOR Mutations in a Patient with an Extraordinary Response on a Phase I Trial of Everolimus and Pazopanib Open
PDF file 249K, Effect of pazopanib on S6K1 phosphorylation in cells expressing activating MTOR mutations
View article: Supplemental Figure 3 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer
Supplemental Figure 3 from The Genomic Landscape of Intrinsic and Acquired Resistance to Cyclin-Dependent Kinase 4/6 Inhibitors in Patients with Hormone Receptor–Positive Metastatic Breast Cancer Open
Figure S3
View article: Supplementary Table S1 from Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting
Supplementary Table S1 from Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting Open
Sample Information: Table with cell line identities and relevant information for this manuscript.
View article: Supplementary Table S2 from Systematic Interrogation of 3q26 Identifies <i>TLOC1</i> and <i>SKIL</i> as Cancer Drivers
Supplementary Table S2 from Systematic Interrogation of 3q26 Identifies <i>TLOC1</i> and <i>SKIL</i> as Cancer Drivers Open
Supplementary Table S2 - XLSX file 1063K, Gene list derived from a gene expression based comparative marker selection between cell lines with normal or amplified levels of 3q26
View article: Supplementary Table 1 from Long-term Benefit of PD-L1 Blockade in Lung Cancer Associated with <i>JAK3</i> Activation
Supplementary Table 1 from Long-term Benefit of PD-L1 Blockade in Lung Cancer Associated with <i>JAK3</i> Activation Open
Table S1: All somatic mutations and short insertion/deletions. This table provides information on all somatic point mutations and short insertion/deletions observed in the tumor sample from this patient. Additional annotations about protei…
View article: Supplementary Methods, Figures S1 - S20 from Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets
Supplementary Methods, Figures S1 - S20 from Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets Open
Supplementary Methods, Figures S1 - S20. Figure S1. Branched evolution leads to tissue-sampling bias in primary tumor samples. Figure S2. Results of ABSOLUTE on samples from patient 418. Figure S3. 2D Bayesian clustering analysis of point-…
View article: Supplementary Legends from Systematic Interrogation of 3q26 Identifies <i>TLOC1</i> and <i>SKIL</i> as Cancer Drivers
Supplementary Legends from Systematic Interrogation of 3q26 Identifies <i>TLOC1</i> and <i>SKIL</i> as Cancer Drivers Open
Supplementary Legends - PDF file 122K, Legends for all Supplementary information